Predicting cell-type-specific gene expression from regions of open chromatin

Genome Research

Volumn 22, Issue 9, 2012, Pages 1711-1722

  Natarajan, Anirudh ^a   Yardimci, Galip Gürkan ^a   Sheffield, Nathan C ^a   Crawford, Gregory E ^a,b   Ohler, Uwe ^a,b  

^a DUKE UNIVERSITY   (United States)

^b DUKE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBONUCLEASE; DEOXYRIBONUCLEASE I; DINUCLEOTIDE;

ARTICLE; CELL TYPE; CELL TYPE SPECIFIC EXPRESSION; CHROMATIN; CONTROLLED STUDY; DNA SEQUENCE; DOWN REGULATION; GENE EXPRESSION; GENETIC ASSOCIATION; GENOMICS; HUMAN; HUMAN CELL; LIVER CELL; PREDICTION; PRIORITY JOURNAL; REGULATORY MECHANISM; UPREGULATION;

BASE COMPOSITION; BINDING SITES; CELL LINE; CHROMATIN ASSEMBLY AND DISASSEMBLY; CLUSTER ANALYSIS; DEOXYRIBONUCLEASE I; DNA FOOTPRINTING; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENOME; HUMANS; ORGAN SPECIFICITY; PROMOTER REGIONS, GENETIC; PROTEIN BINDING; REGULATORY SEQUENCES, NUCLEIC ACID; TRANSCRIPTION FACTORS; TRANSCRIPTION INITIATION SITE;

MAMMALIA;

EID: 84865840434     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.135129.111     Document Type: Article

References (61)

1. Aerts S, Van Loo P, Thijs G, Moreau Y, De Moor B. 2003. Computational detection of cis-regulatory modules. Bioinformatics (Suppl 2) 19: ii5-ii14. (Pubitemid 41296635)
2. Bailey TL, Boden M, Whitington T, Machanick P. 2010. The value of position-specific priors in motif discovery using MEME. BMC Bioinformatics 11: 179. doi: 10.1186/1471-2105-11-179.
3. Bemmo A, Benovoy D, Kwan T, Gaffney DJ, Jensen RV, Majewski J. 2008. Gene expression and isoform variation analysis using Affymetrix Exon Arrays. BMC Genomics 9: 529. doi: 10.1186/1471-2164-9-529.
4. Blow MJ, McCulley DJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F, et al. 2010. ChIP-seq identification of weakly conserved heart enhancers. Nat Genet 42: 806-810.
5. Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, Weng Z, Furey TS, Crawford GE. 2008a. High-resolution mapping and characterization of open chromatin across the genome. Cell 132: 311-322. (Pubitemid 351172431)
6. Boyle AP, Guinney J, Crawford GE, Furey TS. 2008b. F-seq: A feature density estimator for high-throughput sequence tags. Bioinformatics 24: 2537-2538.
7. Boyle AP, Song L, Lee BK, London D, Keefe D, Birney E, Iyer VR, Crawford GE, Furey TS. 2011. High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells. Genome Res 21: 456-464.
8. Britten RJ, Davidson EH. 1969. Gene regulation for higher cells: A theory. Science 165: 349-357.
9. Bryne JC, Valen E, Tang MH, Marstrand T, Winther O, da Piedade I, Krogh A, Lenhard B, Sandelin A. 2008. JASPAR, the open access database of transcription factor-binding profiles: New content and tools in the 2008 update. Nucleic Acids Res 36: D102-D106. (Pubitemid 351149704)
10. Bunt J, Hasselt NE, Zwijnenburg DA, Hamdi M, Koster J, Versteeg R, Kool M. 2011. OTX2 directly activates cell cycle genes and inhibits differentiation in medulloblastoma cells. Int J Cancer 131: E21-E32.
11. Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, Ponjavic J, Semple CA, Taylor MS, Engstrom PG, Frith MC, et al. 2006. Genomewide analysis of mammalian promoter architecture and evolution. Nat Genet 38: 626-635. (Pubitemid 43927303)
12. Cereghini S. 1996. Liver-enriched transcription factors and hepatocyte differentiation. FASEB J 10: 267-282. (Pubitemid 26079946)
13. Chen X, Xu H, Yuan P, Fang F, Huss M, Vega VB, Wong E, Orlov YL, Zhang W, Jiang J, et al. 2008. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133: 1106-1117. (Pubitemid 351787745)
14. Das D, Nahle Z, Zhang MQ. 2006. Adaptively inferring human transcriptional subnetworks. Mol Syst Biol 2: 2006.0029. doi: 10.1038/msb4100067.
15. Fan H, Cinar MU, Phatsara C, Tesfaye D, Tholen E, Looft C, Schellander K. 2011. Molecular mechanism underlying the differential MYF6 expression in postnatal skeletal muscle of Duroc and Pietrain breeds. Gene 486: 8-14.
16. Fu Y, Frith MC, Haverty PM, Weng Z. 2004. MotifViz: An analysis and visualization tool for motif discovery. Nucleic Acids Res 32: W420-W423. (Pubitemid 38997369)
17. Gotea V, Ovcharenko I. 2008. DiRE: Identifying distant regulatory elements of co-expressed genes. Nucleic Acids Res 36: W133-W139.
18. Gotea V, Visel A, Westlund JM, Nobrega MA, Pennacchio LA, Ovcharenko I. 2010. Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers. Genome Res 20: 565-577.
19. Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, Barrera LO, Van Calcar S, Qu C, Ching KA, et al. 2007. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet 39: 311-318. (Pubitemid 46328487)
20. Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, Ye Z, Lee LK, Stuart RK, Ching CW, et al. 2009. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459: 108-112.
21. Hesselberth JR, Chen X, Zhang Z, Sabo PJ, Sandstrom R, Reynolds AP, Thurman RE, Neph S, Kuehn MS, Noble WS, et al. 2009. Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat Methods 6: 283-289.
22. Huang DY, Kuo YY, Chang ZF. 2005. GATA-1 mediates auto-regulation of Gfi-1B transcription in K562 cells. Nucleic Acids Res 33: 5331-5342.
23. Huang DW, Sherman BT, Lempicki RA. 2009a. Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37: 1-13.
24. Huang DW, Sherman BT, Lempicki RA. 2009b. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: 44-57.
25. Johnson WE, Li C, Rabinovic A. 2007. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 8: 118-127. (Pubitemid 44906106)
26. 1-regularized logistic regression. J Mach Learn Res 8: 1519-1555.
27. Kool M, Koster J, Bunt J, Hasselt NE, Lakeman A, van Sluis P, Troost D, Meeteren NS, Caron HN, Cloos J, et al. 2008. Integrated genomics identifies five medulloblastoma subtypes with distinct genetic profiles, pathway signatures and clinicopathological features. PLoS ONE 3: e3088. doi: 10.1371/journal.pone. 0003088.
28. Landolin JM, Johnson DS, Trinklein ND, Aldred SF, Medina C, Shulha H, Weng Z, Myers RM. 2010. Sequence features that drive human promoter function and tissue specificity. Genome Res 20: 890-898.
29. Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
30. Liu H, Schmidt-Supprian M, Shi Y, Hobeika E, Barteneva N, Jumaa H, Pelanda R, Reth M, Skok J, Rajewsky K. 2007. Yin Yang 1 is a critical regulator of B-cell development. Genes Dev 21: 1179-1189. (Pubitemid 46789876)
31. Lu R, Medina KL, Lancki DW, Singh H. 2003. IRF-4,8 orchestrate the pre-B-to-B transition in lymphocyte development. Genes Dev 17: 1703-1708. (Pubitemid 36870333)
32. Ludwig MZ, Palsson A, Alekseeva E, Bergman CM, Nathan J, Kreitman M. 2005. Functional evolution of a cis-regulatory module. PLoS Biol 3: e93. doi: 10.1371/journal.pbio.0030093.
33. Mahony S, Benos PV. 2007. STAMP: A web tool for exploring DNA-binding motif similarities. Nucleic Acids Res 35: W253-W258.
34. Matys V, Kel-Margoulis OV, Fricke E, Liebich I, Land S, Barre-Dirrie A, Reuter I, Chekmenev D, Krull M, Hornischer K, et al. 2006. TRANSFAC and its module TRANSCompel: Transcriptional gene regulation in eukaryotes. Nucleic Acids Res 34: D108-D110.
35. Megraw M, Pereira F, Jensen ST, Ohler U, Hatzigeorgiou AG. 2009. A transcription factor affinity-based code for mammalian transcription initiation. Genome Res 19: 644-656.
36. Newburger DE, Bulyk ML. 2009. UniPROBE: An online database of protein binding microarray data on protein-DNA interactions. Nucleic Acids Res 37: D77-D82.
37. Oda N, Abe M, Sato Y. 1999. ETS-1 converts endothelial cells to the angiogenic phenotype by inducing the expression of matrix metalloproteinases and integrin β3. J Cell Physiol 178: 121-132. (Pubitemid 29034855)
38. Odom DT, Dowell RD, Jacobsen ES, Gordon W, Danford TW, MacIsaac KD, Rolfe PA, Conboy CM, Gifford DK, Fraenkel E. 2007. Tissue-specific transcriptional regulation has diverged significantly between human and mouse. Nat Genet 39: 730-732. (Pubitemid 46848594)
39. Ouyang Z, Zhou Q, Wong WH. 2009. ChIP-seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells. Proc Natl Acad Sci 106: 21521-21526.
40. Pique-Regi R, Degner JF, Pai AA, Gaffney DJ, Gilad Y, Pritchard JK. 2011. Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Res 21: 447-455.
41. Quinlan AR, Hall IM. 2010. BED Tools: A flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841-842.
42. Ramsey SA, Klemm SL, Zak DE, Kennedy KA, Thorsson V, Li B, Gilchrist M, Gold ES, Johnson CD, Litvak V, et al. 2008. Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics. PLoS Comput Biol 4: e1000021. doi: 10.1371/journal.pcbi. 1000021.
43. Rosa A, Brivanlou AH. 2011. A regulatory circuitry comprised of miR-302 and the transcription factors OCT4 and NR2F2 regulates human embryonic stem cell differentiation. EMBO J 30: 237-248.
44. Salomonis N, Schlieve CR, Pereira L, Wahlquist C, Colas A, Zambon AC, Vranizan K, Spindler MJ, Pico AR, Cline MS, et al. 2010. Alternative splicing regulates mouse embryonic stem cell pluripotency and differentiation. Proc Natl Acad Sci 107: 10514-10519.
45. Schoenherr CJ, Anderson DJ. 1995. The neuron-restrictive silencer factor (NRSF): A coordinate repressor of multiple neuron-specific genes. Science 267: 1360-1363.
46. Sharan R, Ovcharenko I, Ben-Hur A, Karp RM. 2003. CREME: A framework for identifying cis-regulatory modules in human-mouse conserved segments. Bioinformatics (Suppl 1) 19: i283-i291.
47. Sinha S, Adler AS, Field Y, Chang HY, Segal E. 2008. Systematic functional characterization of cis-regulatory motifs in human core promoters. Genome Res 18: 477-488. (Pubitemid 351347091)
48. Smith AD, Sumazin P, Zhang MQ. 2005. Identifying tissue-selective transcription factor binding sites in vertebrate promoters. Proc Natl Acad Sci 102: 1560-1565. (Pubitemid 40214367)
49. Sokalski KM, Li SK, Welch I, Cadieux-Pitre HA, Gruca MR, DeKoter RP. 2011. Deletion of genes encoding PU.1 and Spi-B in B cells impairs differentiation and induces pre-B cell acute lymphoblastic leukemia. Blood 118: 2801-2808.
50. Song L, Zhang Z, Grasfeder LL, Boyle AP, Giresi PG, Lee BK, Sheffield NC, Graf S, Huss M, Keefe D, et al. 2011. Open chromatin defined by DNase I and FAIRE identifies regulatory elements that shape cell-type identity. Genome Res 21: 1757-1767.
51. Stormo GD, Zhao Y. 2010. Determining the specificity of protein-DNA interactions. Nat Rev Genet 11: 751-760.
52. Suzuki H, Forrest AR, van Nimwegen E, Daub CO, Balwierz PJ, Irvine KM, Lassmann T, Ravasi T, Hasegawa Y, de Hoon MJ, et al. 2009. The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet 41: 553-562.
53. Takahashi K, Yamanaka S. 2006. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126: 663-676. (Pubitemid 44233629)
54. Thorrez L, Laudadio I, Van Deun K, Quintens R, Hendrickx N, Granvik M, Lemaire K, Schraenen A, Van Lommel L, Lehnert S, et al. 2011. Tissue-specific disallowance of housekeeping genes: The other face of cell differentiation. Genome Res 21: 95-105.
55. van Steensel B, Dekker J. 2010. Genomics tools for unraveling chromosome architecture. Nat Biotechnol 28: 1089-1095.
56. Vavouri T, Elgar G. 2005. Prediction of cis-regulatory elements using binding site matrices - the successes, the failures and the reasons for both. Curr Opin Genet Dev 15: 395-402. (Pubitemid 40982090)
57. Wu C, Gilbert W. 1981. Tissue-specific exposure of chromatin structure at the 5′ terminus of the rat preproinsulin II gene. Proc Natl Acad Sci 78: 1577-1580.
58. Yamashita R, Suzuki Y, Sugano S, Nakai K. 2005. Genome-wide analysis reveals strong correlation between CpG islands with nearby transcription start sites of genes and their tissue specificity. Gene 350: 129-136. (Pubitemid 40719057)
59. Yordy JS, Moussa O, Pei H, Chaussabel D, Li R, Watson DK. 2005. SP100 inhibits ETS1 activity in primary endothelial cells. Oncogene 24: 916-931. (Pubitemid 40216099)
60. Yu J, Vodyanik MA, Smuga-Otto K, Antosiewicz-Bourget J, Frane JL, Tian S, Nie J, Jonsdottir GA, Ruotti V, Stewart R, et al. 2007. Induced pluripotent stem cell lines derived from human somatic cells. Science 318: 1917-1920.
61. Zhu J, He F, Hu S, Yu J. 2008. On the nature of human housekeeping genes. Trends Genet 24: 481-484.